3ANU
Crystal structure of D-serine dehydratase from chicken kidney
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293 | 12-15% PEG 4000, 50mM MES-NaOH, 10% 2-propanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.75 | 55.32 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 104.578 | α = 90 |
b = 104.578 | β = 90 |
c = 81.449 | γ = 90 |
Symmetry | |
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Space Group | P 4 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 95 | CCD | ADSC QUANTUM 315r | 2010-03-12 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-5A | 1.0000, 1.28179, 1.28284, 1.25510, 1.30300 | Photon Factory | BL-5A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | |||||||||
1 | 1.9 | 17 | 99.2 | 26.5 | 6.9 | 36209 | 35919 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 1.9 | 2 | 99.7 | 3.5 | 6.7 | 5021 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MAD | THROUGHOUT | 1.9 | 17 | 34123 | 34123 | 1796 | 100 | 0.19035 | 0.19035 | 0.18906 | 0.21486 | RANDOM | 35.334 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-1.4 | -1.4 | 2.8 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.414 |
r_dihedral_angle_4_deg | 16.255 |
r_dihedral_angle_3_deg | 14.882 |
r_dihedral_angle_1_deg | 5.873 |
r_scangle_it | 3.108 |
r_scbond_it | 1.894 |
r_angle_refined_deg | 1.309 |
r_mcangle_it | 1.176 |
r_mcbond_it | 0.647 |
r_chiral_restr | 0.096 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2778 |
Nucleic Acid Atoms | |
Solvent Atoms | 143 |
Heterogen Atoms | 17 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
SHARP | phasing |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |